Table 7.

Comparison of the main steps and features of conventional molecular mutation detection methods

Method	Unknown mutation	Quantitative	Amplification	Differentiation	Detection	Advantages	Disadvantages
PCR-SERS in this paper	-	+	multiplex PCR with mutation-specific probes	tags on probes	SERS	rapid multiplex detection, high sensitivity, simple data analysis	uniform SERS substrate
Multiplex PCR	-	-	PCR with multiple pairs of primers	size differences	electrophoresis	reduces time and labor requirements	low sensitivity and specificity
Real-time PCR	-	+	PCR amplicon is monitored as the PCR progresses	tags on probes	fluorescence	high sensitivity, can be multiplexed, no post-PCR analysis, simple data analysis	expensive in equipment and staff training
ARMS	-	-	allele-specific amplification	size differences, tags on primers	electrophoresis, fluorescence	high sensitivity, quick, inexpensive, simple to devise	high cost
Ligation assay	-	-	primers annealed to adjacent sites	tags on primers	fluorescence	can be multiplexed, can be used on a single nucleotide or a few adjacent nucleotides	linear amplification rather than exponential one
Sequencing	+	+	PCR amplicon used as the template	tags on the dideoxynucleotide	fluorescence, mass spectroscopy	a “gold standard” mutation screening technique, high-throughput, high-accuracy	expensive
Single strand conformational polymorphism (SSCP)	+	-	optional PCR	different DNA conformation	fluorescence, electrophoresis	high sensitivity, detects close to 100% of point mutations	complex
Denaturing gradient gel electrophoresis (DGGE)	+	-	optional PCR	different melting behavior	fluorescence, electrophoresis	high sensitivity, detects ~80-90% of point mutations	low throughput, complex primer design